As for human emotional signals in aliens--I always thought it was a very nice touch by Leonard Nimoy, or whoever was responsible, in "Enterprise Incident," to establish that Vulcans and Rommies don't kiss with their mouths. (Not to suggest that it is a problem in ST11 that they do; he's getting it with a human, who wouldn't get much of a kick out of holding hands).
Still, TV production realities force human emotional signals in aliens, and that's okay. There is no economical way around it to do the kinds of stories Trek wants to tell.
Worse is the Trek misunderstanding of how biological systems evolve.
In "The Chase," I wish so much that they hadn't gone for the bleachers with their binding of the various humanoid species. What's wrong with leaving the Progenitors as the force who had enforced a galactic standard of DNA over other replicators, creating an oh-so distant, but still palpable, kinship link between all (except the Horta, and the Tholians, and the Sheliak, I guess
)? This isn't implausible--it leaves open the question of their motives, but the actual act is not so unlikely and difficult to perform that it raises questions of practicality.
I find it difficult to fathom how they were supposed to "program" bipedality, large brain size, and a mouth that allows food to stupidly pass over the airway (choked on my dinner out earlier tonight, thanks a lot Salome Jens and our terrestrial vertebrate common ancestor! <_< ) into the chemistry, when that chemistry is simply not there at that point in time. I mean, if you programmed that which makes us humanoid into DNA, the DNA would express itself (in the appropriate environment) as... well, a humanoid. Not a proto-humanoid. Not an ancient protist that will one day lead to humanoids. A humanoid. Lacking an appropriate environment, of course, the Progenitors presumably just left a bunch of dead fetilized eggs all over the galaxy.
Further, while an ecology based on a DNA/RNA regime definitely can lead to bipedality, etc., under some circumstances--obviously, here we are--it would not, necessarily, under every circumstance. If the wisdom of the Progenitors is such that they could reliably predict the outcome of such a chaotic system as hundreds or thousands of biospheres operating over billions of years, so that they could influence the initial conditions to make humanoids, then it raises the question: why didn't they just make humanoids
There are also critical ethical questions about permitting the savagery of all natural and social history to take place when it wasn't really necessary.
Trek is really
into the idea that evolutionary potential is already inside us, like a hidden item in a video game, "locked away" until we go down the proper pipe. It's the free radicals, radiation, randomness, time and above all the context of our environments that shape us. From the entertainingly egregious scientific illiteracy of "Genesis," to the fun fable, marred by the traditional Trek tactic of fixing an implausibility problem with an even more implausible solution, of "The Chase," to the truly sickening ideological implications of "Dear Doctor," Trek seems to believe wholeheartedly in this entirely ridiculous, conceivably dangerous position.